Variant 4-69098619-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_001074.4(UGT2B7):c.801A>T(p.Pro267=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.501 in 1,610,220 control chromosomes in the GnomAD database, including 209,131 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.58 ( 25991 hom., cov: 30)

Exomes 𝑓: 0.49 ( 183140 hom. )

Consequence

UGT2B7
NM_001074.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.613

Variant links:

Genes affected

UGT2B7 (HGNC:12554): (UDP glucuronosyltransferase family 2 member B7) The protein encoded by this gene belongs to the UDP-glycosyltransferase (UGT) family. UGTs serve a major role in the conjugation and subsequent elimination of potentially toxic xenobiotics and endogenous compounds. This protein is localized in the microsome membrane, and has unique specificity for 3,4-catechol estrogens and estriol, suggesting that it may play an important role in regulating the level and activity of these potent estrogen metabolites. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]

UGT2B7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP7

Synonymous conserved (PhyloP=-0.613 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.705 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein
UGT2B7	NM_001074.4 linkuse as main transcript	c.801A>T	p.Pro267=	synonymous_variant	2/6	ENST00000305231.12	NP_001065.2
UGT2B7	NM_001330719.2 linkuse as main transcript	c.801A>T	p.Pro267=	synonymous_variant	2/5		NP_001317648.1
UGT2B7	NM_001349568.2 linkuse as main transcript	c.54A>T	p.Pro18=	synonymous_variant	3/7		NP_001336497.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UGT2B7	ENST00000305231.12 linkuse as main transcript	c.801A>T	p.Pro267=	synonymous_variant	2/6	1	NM_001074.4	ENSP00000304811	P1

Frequencies

GnomAD3 genomes

AF:

0.575

AC:

86867

AN:

150948

Hom.:

25945

Cov.:

show subpopulations

Gnomad AFR

AF:

0.712

Gnomad AMI

AF:

0.485

Gnomad AMR

AF:

0.659

Gnomad ASJ

AF:

0.512

Gnomad EAS

AF:

0.698

Gnomad SAS

AF:

0.603

Gnomad FIN

AF:

0.573

Gnomad MID

AF:

0.576

Gnomad NFE

AF:

0.468

Gnomad OTH

AF:

0.586

GnomAD3 exomes

AF:

0.564

AC:

140796

AN:

249522

Hom.:

41188

AF XY:

0.554

AC XY:

74773

AN XY:

134994

show subpopulations

Gnomad AFR exome

AF:

0.714

Gnomad AMR exome

AF:

0.720

Gnomad ASJ exome

AF:

0.508

Gnomad EAS exome

AF:

0.704

Gnomad SAS exome

AF:

0.570

Gnomad FIN exome

AF:

0.583

Gnomad NFE exome

AF:

0.475

Gnomad OTH exome

AF:

0.539

GnomAD4 exome

AF:

0.494

AC:

720449

AN:

1459152

Hom.:

183140

Cov.:

AF XY:

0.495

AC XY:

359018

AN XY:

725794

show subpopulations

Gnomad4 AFR exome

AF:

0.716

Gnomad4 AMR exome

AF:

0.713

Gnomad4 ASJ exome

AF:

0.509

Gnomad4 EAS exome

AF:

0.703

Gnomad4 SAS exome

AF:

0.567

Gnomad4 FIN exome

AF:

0.578

Gnomad4 NFE exome

AF:

0.459

Gnomad4 OTH exome

AF:

0.517

GnomAD4 genome

AF:

0.576

AC:

86968

AN:

151068

Hom.:

25991

Cov.:

AF XY:

0.584

AC XY:

43107

AN XY:

73760

show subpopulations

Gnomad4 AFR

AF:

0.712

Gnomad4 AMR

AF:

0.659

Gnomad4 ASJ

AF:

0.512

Gnomad4 EAS

AF:

0.697

Gnomad4 SAS

AF:

0.604

Gnomad4 FIN

AF:

0.573

Gnomad4 NFE

AF:

0.468

Gnomad4 OTH

AF:

0.586

Alfa

AF:

0.497

Hom.:

6217

Bravo

AF:

0.590

Asia WGS

AF:

0.655

AC:

2275

AN:

3478

EpiCase

AF:

0.490

EpiControl

AF:

0.481

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.42

DANN

Benign

0.60

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over